DE analysis
DE_res <- DE_analysis(ls_preprocessed,
GeneBased=TRUE,
pDataBased=FALSE,
NewCondition=FALSE,
cond_nm='ENSG00000151012.9',
reference = 'low',
correct_gender=TRUE,
extremes_only=TRUE)
## Unlist done
## Labeling done
## Filtering done
## factor levels were dropped which had no samples
## Design done
## factor levels were dropped which had no samples
## Warning: Setting row names on a tibble is deprecated.
## vsd symbols done
## using pre-existing size factors
## estimating dispersions
## gene-wise dispersion estimates
## mean-dispersion relationship
## final dispersion estimates
## fitting model and testing
## -- replacing outliers and refitting for 1895 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)
## estimating dispersions
## fitting model and testing
## DESeq done
## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895
## res symbols done
## list done
DE results
heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)

x <- DE_res$res_df %>%
arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- c('ENSG00000250033.1', 'ENSG00000151012.9')
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='SLC7A11', pCutoff=0.001, FCcutoff=1.5)

List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)
vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)
| 74.190171 |
3.405788 |
0.2970759 |
3.381561 |
0.0007208 |
0.0278326 |
ENSG00000070985.9 |
TRPM5 |
FC_P |
TRPM5 |
3.405788 |
0.0007208 |
| 459.330155 |
3.027988 |
0.3489373 |
8.916714 |
0.0000000 |
0.0000000 |
ENSG00000272405.1 |
RP11-284F21.10 |
FC_P |
RP11.284F21.10 |
3.027988 |
0.0000000 |
| 7427.904523 |
3.006456 |
0.3492571 |
8.836991 |
0.0000000 |
0.0000000 |
ENSG00000187134.8 |
AKR1C1 |
FC_P |
AKR1C1 |
3.006456 |
0.0000000 |
| 232.584131 |
2.999641 |
0.3634148 |
8.670954 |
0.0000000 |
0.0000000 |
ENSG00000272068.1 |
RP11-284F21.9 |
FC_P |
RP11.284F21.9 |
2.999641 |
0.0000000 |
| 479.119508 |
2.981368 |
0.3392760 |
8.829212 |
0.0000000 |
0.0000000 |
ENSG00000171658.4 |
RP11-443P15.2 |
FC_P |
RP11.443P15.2 |
2.981368 |
0.0000000 |
| 45.882785 |
2.844477 |
0.3685875 |
8.175402 |
0.0000000 |
0.0000000 |
ENSG00000267354.1 |
RP11-749H17.2 |
FC_P |
RP11.749H17.2 |
2.844477 |
0.0000000 |
| 347.932687 |
2.805225 |
0.3518530 |
8.121889 |
0.0000000 |
0.0000000 |
ENSG00000132874.9 |
SLC14A2 |
FC_P |
SLC14A2 |
2.805225 |
0.0000000 |
| 3.559773 |
2.648320 |
0.3759864 |
4.796590 |
0.0000016 |
0.0004034 |
ENSG00000223440.1 |
RP11-555J4.4 |
FC_P |
RP11.555J4.4 |
2.648320 |
0.0000016 |
| 123.368039 |
2.584478 |
0.3725841 |
7.494079 |
0.0000000 |
0.0000000 |
ENSG00000266968.1 |
RP11-116O18.1 |
FC_P |
RP11.116O18.1 |
2.584478 |
0.0000000 |
| 279.531205 |
2.546159 |
0.3487764 |
7.071791 |
0.0000000 |
0.0000000 |
ENSG00000186529.10 |
CYP4F3 |
FC_P |
CYP4F3 |
2.546159 |
0.0000000 |
| 4.882729 |
2.503333 |
0.3766314 |
4.880883 |
0.0000011 |
0.0002733 |
ENSG00000230516.1 |
RP11-555J4.3 |
FC_P |
RP11.555J4.3 |
2.503333 |
0.0000011 |
| 1651.565726 |
2.497583 |
0.3473948 |
7.235067 |
0.0000000 |
0.0000000 |
ENSG00000074410.9 |
CA12 |
FC_P |
CA12 |
2.497583 |
0.0000000 |
| 870.137624 |
2.465815 |
0.3498300 |
7.118855 |
0.0000000 |
0.0000000 |
ENSG00000023839.6 |
ABCC2 |
FC_P |
ABCC2 |
2.465815 |
0.0000000 |
| 874.243059 |
2.463836 |
0.3688451 |
7.025027 |
0.0000000 |
0.0000000 |
ENSG00000188517.10 |
COL25A1 |
FC_P |
COL25A1 |
2.463836 |
0.0000000 |
| 121.539700 |
2.435846 |
0.3596729 |
6.978479 |
0.0000000 |
0.0000000 |
ENSG00000266988.1 |
RP11-749H17.1 |
FC_P |
RP11.749H17.1 |
2.435846 |
0.0000000 |
| 204.766447 |
2.424232 |
0.3165917 |
7.738857 |
0.0000000 |
0.0000000 |
ENSG00000132692.14 |
BCAN |
FC_P |
BCAN |
2.424232 |
0.0000000 |
| 1495.204721 |
2.399995 |
0.3443518 |
7.320679 |
0.0000000 |
0.0000000 |
ENSG00000154277.8 |
UCHL1 |
FC_P |
UCHL1 |
2.399995 |
0.0000000 |
| 62.349552 |
2.382709 |
0.3475235 |
6.891168 |
0.0000000 |
0.0000000 |
ENSG00000229953.1 |
RP11-284F21.7 |
FC_P |
RP11.284F21.7 |
2.382709 |
0.0000000 |
| 6545.823063 |
2.371212 |
0.3765497 |
7.174525 |
0.0000000 |
0.0000000 |
ENSG00000021826.10 |
CPS1 |
FC_P |
CPS1 |
2.371212 |
0.0000000 |
| 465.695914 |
2.366098 |
0.3562091 |
6.746753 |
0.0000000 |
0.0000000 |
ENSG00000198732.6 |
SMOC1 |
FC_P |
SMOC1 |
2.366098 |
0.0000000 |
| 38.733029 |
2.343681 |
0.3502032 |
6.947071 |
0.0000000 |
0.0000000 |
ENSG00000260253.1 |
RP4-676L2.1 |
FC_P |
RP4.676L2.1 |
2.343681 |
0.0000000 |
| 80.438655 |
2.342847 |
0.3183119 |
4.513350 |
0.0000064 |
0.0011696 |
ENSG00000123999.4 |
INHA |
FC_P |
INHA |
2.342847 |
0.0000064 |
| 110.170354 |
-2.341944 |
0.3508471 |
-4.112740 |
0.0000391 |
0.0043567 |
ENSG00000142319.14 |
SLC6A3 |
FC_P |
SLC6A3 |
-2.341944 |
0.0000391 |
| 88.568776 |
2.322626 |
0.3301606 |
3.988584 |
0.0000665 |
0.0062198 |
ENSG00000111432.4 |
FZD10 |
FC_P |
FZD10 |
2.322626 |
0.0000665 |
| 29.331747 |
2.306891 |
0.3754437 |
6.805462 |
0.0000000 |
0.0000000 |
ENSG00000223784.1 |
RP11-554I8.2 |
FC_P |
RP11.554I8.2 |
2.306891 |
0.0000000 |
| 1274.086656 |
2.305160 |
0.3689645 |
7.243346 |
0.0000000 |
0.0000000 |
ENSG00000163993.6 |
S100P |
FC_P |
S100P |
2.305160 |
0.0000000 |
| 362.457374 |
2.288372 |
0.3708839 |
6.370850 |
0.0000000 |
0.0000002 |
ENSG00000145920.10 |
CPLX2 |
FC_P |
CPLX2 |
2.288372 |
0.0000000 |
| 993.442925 |
2.286053 |
0.3768588 |
7.832738 |
0.0000000 |
0.0000000 |
ENSG00000198074.5 |
AKR1B10 |
FC_P |
AKR1B10 |
2.286053 |
0.0000000 |
| 642.005472 |
2.282440 |
0.3658758 |
6.538870 |
0.0000000 |
0.0000001 |
ENSG00000162006.5 |
MSLNL |
FC_P |
MSLNL |
2.282440 |
0.0000000 |
| 10.306929 |
2.277901 |
0.3759199 |
5.799766 |
0.0000000 |
0.0000037 |
ENSG00000237922.1 |
RP11-478H16.1 |
FC_P |
RP11.478H16.1 |
2.277901 |
0.0000000 |
| 4.431762 |
-2.258036 |
0.3088657 |
-3.954290 |
0.0000768 |
0.0066699 |
ENSG00000264169.1 |
RN7SL665P |
FC_P |
RN7SL665P |
-2.258036 |
0.0000768 |
| 694.601993 |
2.251461 |
0.3494746 |
6.537153 |
0.0000000 |
0.0000001 |
ENSG00000113924.7 |
HGD |
FC_P |
HGD |
2.251461 |
0.0000000 |
| 50.160905 |
2.233866 |
0.3770108 |
6.607034 |
0.0000000 |
0.0000001 |
ENSG00000204529.3 |
GUCY2EP |
FC_P |
GUCY2EP |
2.233866 |
0.0000000 |
| 59.794339 |
2.225074 |
0.3589528 |
4.201972 |
0.0000265 |
0.0032623 |
ENSG00000234854.1 |
LINC00676 |
FC_P |
LINC00676 |
2.225074 |
0.0000265 |
| 30.274878 |
2.214739 |
0.3769530 |
6.506383 |
0.0000000 |
0.0000001 |
ENSG00000150201.10 |
FXYD4 |
FC_P |
FXYD4 |
2.214739 |
0.0000000 |
| 529.247003 |
2.210036 |
0.3661251 |
5.881068 |
0.0000000 |
0.0000024 |
ENSG00000171903.12 |
CYP4F11 |
FC_P |
CYP4F11 |
2.210036 |
0.0000000 |
| 294.213510 |
2.204818 |
0.3007350 |
4.931953 |
0.0000008 |
0.0002238 |
ENSG00000188385.7 |
JAKMIP3 |
FC_P |
JAKMIP3 |
2.204818 |
0.0000008 |
| 72.955735 |
2.148765 |
0.3614406 |
6.069562 |
0.0000000 |
0.0000009 |
ENSG00000238840.1 |
U8 |
FC_P |
U8 |
2.148765 |
0.0000000 |
| 15.310757 |
2.119574 |
0.3767345 |
5.995955 |
0.0000000 |
0.0000013 |
ENSG00000266670.1 |
RN7SL637P |
FC_P |
RN7SL637P |
2.119574 |
0.0000000 |
| 1395.160446 |
2.112028 |
0.3456262 |
6.104160 |
0.0000000 |
0.0000008 |
ENSG00000163053.6 |
SLC16A14 |
FC_P |
SLC16A14 |
2.112028 |
0.0000000 |
| 82.463824 |
2.099401 |
0.3182834 |
6.569299 |
0.0000000 |
0.0000001 |
ENSG00000169684.9 |
CHRNA5 |
FC_P |
CHRNA5 |
2.099401 |
0.0000000 |
| 181.893588 |
2.096907 |
0.3563406 |
5.951120 |
0.0000000 |
0.0000017 |
ENSG00000206633.1 |
SNORA80B |
FC_P |
SNORA80B |
2.096907 |
0.0000000 |
| 76.409511 |
2.077665 |
0.3762764 |
6.370548 |
0.0000000 |
0.0000002 |
ENSG00000254632.1 |
RP11-21L23.4 |
FC_P |
RP11.21L23.4 |
2.077665 |
0.0000000 |
| 6371.061506 |
2.071104 |
0.3291870 |
6.305977 |
0.0000000 |
0.0000003 |
ENSG00000115758.8 |
ODC1 |
FC_P |
ODC1 |
2.071104 |
0.0000000 |
| 375.318850 |
2.065094 |
0.3349679 |
6.265065 |
0.0000000 |
0.0000003 |
ENSG00000151322.14 |
NPAS3 |
FC_P |
NPAS3 |
2.065094 |
0.0000000 |
| 230.710001 |
2.063787 |
0.3574696 |
5.982812 |
0.0000000 |
0.0000014 |
ENSG00000074211.9 |
PPP2R2C |
FC_P |
PPP2R2C |
2.063787 |
0.0000000 |
| 17.948421 |
2.036933 |
0.3736248 |
4.989893 |
0.0000006 |
0.0001779 |
ENSG00000160182.2 |
TFF1 |
FC_P |
TFF1 |
2.036933 |
0.0000006 |
| 3379.164215 |
2.031917 |
0.3081060 |
6.658004 |
0.0000000 |
0.0000000 |
ENSG00000181019.8 |
NQO1 |
FC_P |
NQO1 |
2.031917 |
0.0000000 |
| 71.367166 |
2.031584 |
0.3753486 |
5.822359 |
0.0000000 |
0.0000033 |
ENSG00000258346.1 |
RP11-148B3.2 |
FC_P |
RP11.148B3.2 |
2.031584 |
0.0000000 |
| 17.710673 |
2.029457 |
0.3718034 |
3.410167 |
0.0006492 |
0.0259320 |
ENSG00000258657.1 |
RP11-104E19.1 |
FC_P |
RP11.104E19.1 |
2.029457 |
0.0006492 |
| 1402.099877 |
2.025799 |
0.3683234 |
5.713581 |
0.0000000 |
0.0000055 |
ENSG00000081277.7 |
PKP1 |
FC_P |
PKP1 |
2.025799 |
0.0000000 |
| 1046.315215 |
2.022021 |
0.3444501 |
5.946139 |
0.0000000 |
0.0000017 |
ENSG00000006016.6 |
CRLF1 |
FC_P |
CRLF1 |
2.022021 |
0.0000000 |
| 2.508772 |
2.020757 |
0.3764879 |
5.375034 |
0.0000001 |
0.0000304 |
ENSG00000267909.1 |
CCDC177 |
FC_P |
CCDC177 |
2.020757 |
0.0000001 |
| 2428.113741 |
2.005371 |
0.3154303 |
6.305759 |
0.0000000 |
0.0000003 |
ENSG00000159228.8 |
CBR1 |
FC_P |
CBR1 |
2.005371 |
0.0000000 |
| 37.599176 |
2.002212 |
0.3574304 |
3.349147 |
0.0008106 |
0.0301553 |
ENSG00000101076.12 |
HNF4A |
FC_P |
HNF4A |
2.002212 |
0.0008106 |
| 255.242400 |
1.996612 |
0.3732896 |
6.206375 |
0.0000000 |
0.0000004 |
ENSG00000196091.8 |
MYBPC1 |
FC_P |
MYBPC1 |
1.996612 |
0.0000000 |
| 3.302264 |
1.987676 |
0.3762094 |
5.588683 |
0.0000000 |
0.0000107 |
ENSG00000249199.1 |
CTD-2139B15.5 |
FC_P |
CTD.2139B15.5 |
1.987676 |
0.0000000 |
| 19.305845 |
1.976134 |
0.3762142 |
5.567895 |
0.0000000 |
0.0000118 |
ENSG00000237937.1 |
AP000770.1 |
FC_P |
AP000770.1 |
1.976134 |
0.0000000 |
| 10.903050 |
1.972538 |
0.3751092 |
6.067071 |
0.0000000 |
0.0000009 |
ENSG00000164089.4 |
ETNPPL |
FC_P |
ETNPPL |
1.972538 |
0.0000000 |
| 95.226916 |
1.972021 |
0.3521824 |
5.041675 |
0.0000005 |
0.0001415 |
ENSG00000156755.9 |
IGKV1OR-2 |
FC_P |
IGKV1OR.2 |
1.972021 |
0.0000005 |
| 160.927856 |
1.969863 |
0.3619607 |
4.344289 |
0.0000140 |
0.0020543 |
ENSG00000171759.4 |
PAH |
FC_P |
PAH |
1.969863 |
0.0000140 |
| 194.766130 |
1.968949 |
0.3570444 |
5.549415 |
0.0000000 |
0.0000128 |
ENSG00000174473.11 |
GALNTL6 |
FC_P |
GALNTL6 |
1.968949 |
0.0000000 |
| 50.443154 |
1.954590 |
0.3676189 |
5.376872 |
0.0000001 |
0.0000304 |
ENSG00000237810.3 |
CTD-2571E19.3 |
FC_P |
CTD.2571E19.3 |
1.954590 |
0.0000001 |
| 21.973522 |
1.950368 |
0.3748841 |
6.086028 |
0.0000000 |
0.0000008 |
ENSG00000238001.2 |
RP11-555J4.2 |
FC_P |
RP11.555J4.2 |
1.950368 |
0.0000000 |
| 69.201905 |
1.945125 |
0.3760332 |
5.245463 |
0.0000002 |
0.0000587 |
ENSG00000267056.2 |
AC005336.4 |
FC_P |
AC005336.4 |
1.945125 |
0.0000002 |
| 21.896080 |
1.935212 |
0.3732443 |
5.238493 |
0.0000002 |
0.0000598 |
ENSG00000199400.1 |
RNY4P19 |
FC_P |
RNY4P19 |
1.935212 |
0.0000002 |
| 209.780583 |
1.928813 |
0.3432631 |
5.569095 |
0.0000000 |
0.0000118 |
ENSG00000166206.9 |
GABRB3 |
FC_P |
GABRB3 |
1.928813 |
0.0000000 |
| 8.383895 |
1.925363 |
0.3733169 |
6.059844 |
0.0000000 |
0.0000009 |
ENSG00000266952.1 |
RP11-909B2.1 |
FC_P |
RP11.909B2.1 |
1.925363 |
0.0000000 |
| 866.222931 |
1.917266 |
0.2860782 |
6.760482 |
0.0000000 |
0.0000000 |
ENSG00000176153.10 |
GPX2 |
FC_P |
GPX2 |
1.917266 |
0.0000000 |
| 21.006391 |
1.913548 |
0.3622107 |
5.380539 |
0.0000001 |
0.0000301 |
ENSG00000248802.1 |
RP11-184M15.2 |
FC_P |
RP11.184M15.2 |
1.913548 |
0.0000001 |
| 87.069743 |
1.913200 |
0.3207755 |
5.943249 |
0.0000000 |
0.0000017 |
ENSG00000268657.1 |
AL133373.1 |
FC_P |
AL133373.1 |
1.913200 |
0.0000000 |
| 619.702039 |
1.912097 |
0.3328342 |
5.638360 |
0.0000000 |
0.0000082 |
ENSG00000160211.11 |
G6PD |
FC_P |
G6PD |
1.912097 |
0.0000000 |
| 219.862687 |
1.880657 |
0.3468073 |
5.493415 |
0.0000000 |
0.0000171 |
ENSG00000105696.4 |
TMEM59L |
FC_P |
TMEM59L |
1.880657 |
0.0000000 |
| 834.025114 |
1.880009 |
0.3763159 |
6.216487 |
0.0000000 |
0.0000004 |
ENSG00000125851.5 |
PCSK2 |
FC_P |
PCSK2 |
1.880009 |
0.0000000 |
| 1320.572201 |
1.877303 |
0.3352290 |
5.617172 |
0.0000000 |
0.0000092 |
ENSG00000196208.9 |
GREB1 |
FC_P |
GREB1 |
1.877303 |
0.0000000 |
| 857.358271 |
1.875697 |
0.3767609 |
5.955880 |
0.0000000 |
0.0000017 |
ENSG00000223414.2 |
LINC00473 |
FC_P |
LINC00473 |
1.875697 |
0.0000000 |
| 15.339345 |
1.868028 |
0.3521888 |
5.257173 |
0.0000001 |
0.0000556 |
ENSG00000235010.1 |
RP11-140A10.3 |
FC_P |
RP11.140A10.3 |
1.868028 |
0.0000001 |
| 1011.557633 |
1.864581 |
0.3281571 |
5.784366 |
0.0000000 |
0.0000039 |
ENSG00000088992.13 |
TESC |
FC_P |
TESC |
1.864581 |
0.0000000 |
| 28.704369 |
-1.858401 |
0.3742610 |
-4.989742 |
0.0000006 |
0.0001779 |
ENSG00000253998.2 |
IGKV2-29 |
FC_P |
IGKV2.29 |
-1.858401 |
0.0000006 |
| 26.352033 |
1.855965 |
0.2869215 |
6.435439 |
0.0000000 |
0.0000001 |
ENSG00000238266.1 |
LINC00707 |
FC_P |
LINC00707 |
1.855965 |
0.0000000 |
| 241.237536 |
1.843452 |
0.3741078 |
6.405012 |
0.0000000 |
0.0000002 |
ENSG00000256391.1 |
SDIM1 |
FC_P |
SDIM1 |
1.843452 |
0.0000000 |
| 6.520975 |
1.839244 |
0.3670198 |
4.975890 |
0.0000006 |
0.0001881 |
ENSG00000213877.3 |
CFL1P7 |
FC_P |
CFL1P7 |
1.839244 |
0.0000006 |
| 3590.008024 |
1.838267 |
0.3210254 |
5.721048 |
0.0000000 |
0.0000053 |
ENSG00000108551.4 |
RASD1 |
FC_P |
RASD1 |
1.838267 |
0.0000000 |
| 459.443327 |
1.833677 |
0.3605677 |
5.212133 |
0.0000002 |
0.0000681 |
ENSG00000130234.6 |
ACE2 |
FC_P |
ACE2 |
1.833677 |
0.0000002 |
| 7491.793041 |
1.825854 |
0.3656628 |
5.129465 |
0.0000003 |
0.0000973 |
ENSG00000102854.10 |
MSLN |
FC_P |
MSLN |
1.825854 |
0.0000003 |
| 389.824841 |
1.816518 |
0.2906246 |
6.269368 |
0.0000000 |
0.0000003 |
ENSG00000154040.16 |
CABYR |
FC_P |
CABYR |
1.816518 |
0.0000000 |
| 455.267267 |
1.803813 |
0.3770193 |
5.392606 |
0.0000001 |
0.0000288 |
ENSG00000173702.3 |
MUC13 |
FC_P |
MUC13 |
1.803813 |
0.0000001 |
| 54.320259 |
1.787927 |
0.3709747 |
6.165040 |
0.0000000 |
0.0000006 |
ENSG00000254761.1 |
RP11-672A2.1 |
FC_P |
RP11.672A2.1 |
1.787927 |
0.0000000 |
| 47.113664 |
1.769783 |
0.3395574 |
4.937011 |
0.0000008 |
0.0002210 |
ENSG00000103154.5 |
NECAB2 |
FC_P |
NECAB2 |
1.769783 |
0.0000008 |
| 11.489322 |
1.754215 |
0.3709195 |
4.909610 |
0.0000009 |
0.0002432 |
ENSG00000261146.1 |
RP11-2A4.4 |
FC_P |
RP11.2A4.4 |
1.754215 |
0.0000009 |
| 124.663437 |
1.748197 |
0.3201227 |
5.486194 |
0.0000000 |
0.0000176 |
ENSG00000138152.7 |
BTBD16 |
FC_P |
BTBD16 |
1.748197 |
0.0000000 |
| 6.366272 |
-1.746772 |
0.3679698 |
-4.403550 |
0.0000106 |
0.0017046 |
ENSG00000235712.6 |
RXRB |
FC_P |
RXRB |
-1.746772 |
0.0000106 |
| 31.092473 |
1.740834 |
0.3028418 |
5.746033 |
0.0000000 |
0.0000048 |
ENSG00000227184.3 |
EPPK1 |
FC_P |
EPPK1 |
1.740834 |
0.0000000 |
| 35.256486 |
-1.740491 |
0.3529971 |
-4.750027 |
0.0000020 |
0.0004883 |
ENSG00000249320.1 |
RP11-206P5.1 |
FC_P |
RP11.206P5.1 |
-1.740491 |
0.0000020 |
| 114.416012 |
1.732618 |
0.3581048 |
4.261021 |
0.0000203 |
0.0027303 |
ENSG00000086159.8 |
AQP6 |
FC_P |
AQP6 |
1.732618 |
0.0000203 |
| 4000.175504 |
1.726165 |
0.2671587 |
6.482953 |
0.0000000 |
0.0000001 |
ENSG00000109814.7 |
UGDH |
FC_P |
UGDH |
1.726165 |
0.0000000 |
| 7.630741 |
1.723931 |
0.3768766 |
4.678865 |
0.0000029 |
0.0006419 |
ENSG00000254975.1 |
RP11-672A2.3 |
FC_P |
RP11.672A2.3 |
1.723931 |
0.0000029 |
| 6.528918 |
1.720410 |
0.3702455 |
4.720316 |
0.0000024 |
0.0005455 |
ENSG00000237838.1 |
AC133680.1 |
FC_P |
AC133680.1 |
1.720410 |
0.0000024 |
| 6.637467 |
1.708287 |
0.3765066 |
4.949911 |
0.0000007 |
0.0002100 |
ENSG00000231295.1 |
RP4-797C5.2 |
FC_P |
RP4.797C5.2 |
1.708287 |
0.0000007 |
| 47.601009 |
1.702250 |
0.3530480 |
4.736376 |
0.0000022 |
0.0005168 |
ENSG00000179477.5 |
ALOX12B |
FC_P |
ALOX12B |
1.702250 |
0.0000022 |
| 11.504493 |
1.700148 |
0.3589490 |
4.763558 |
0.0000019 |
0.0004628 |
ENSG00000235899.1 |
RP11-345L23.1 |
FC_P |
RP11.345L23.1 |
1.700148 |
0.0000019 |
| 7.118675 |
1.694329 |
0.3690801 |
4.592801 |
0.0000044 |
0.0008775 |
ENSG00000224409.1 |
RP11-114B7.6 |
FC_P |
RP11.114B7.6 |
1.694329 |
0.0000044 |
| 66.019409 |
1.691193 |
0.3227927 |
5.121348 |
0.0000003 |
0.0001006 |
ENSG00000080644.11 |
CHRNA3 |
FC_P |
CHRNA3 |
1.691193 |
0.0000003 |
| 21.569154 |
1.686967 |
0.3450868 |
4.807041 |
0.0000015 |
0.0003855 |
ENSG00000261762.1 |
RP11-650L12.2 |
FC_P |
RP11.650L12.2 |
1.686967 |
0.0000015 |
| 400.284587 |
1.681043 |
0.2796218 |
5.948558 |
0.0000000 |
0.0000017 |
ENSG00000108448.16 |
TRIM16L |
FC_P |
TRIM16L |
1.681043 |
0.0000000 |
| 72.167854 |
1.680654 |
0.3447147 |
4.560148 |
0.0000051 |
0.0009818 |
ENSG00000132437.13 |
DDC |
FC_P |
DDC |
1.680654 |
0.0000051 |
| 954.309668 |
1.673960 |
0.2362214 |
3.528497 |
0.0004179 |
0.0198333 |
ENSG00000182704.6 |
TSKU |
FC_P |
TSKU |
1.673960 |
0.0004179 |
| 98.576368 |
-1.671048 |
0.3411904 |
-5.182546 |
0.0000002 |
0.0000776 |
ENSG00000164530.9 |
PI16 |
FC_P |
PI16 |
-1.671048 |
0.0000002 |
| 4.408143 |
1.665405 |
0.3658897 |
4.468331 |
0.0000079 |
0.0013468 |
ENSG00000215124.2 |
RP3-420J14.1 |
FC_P |
RP3.420J14.1 |
1.665405 |
0.0000079 |
| 16736.465458 |
1.664487 |
0.3770252 |
4.734241 |
0.0000022 |
0.0005177 |
ENSG00000096088.12 |
PGC |
FC_P |
PGC |
1.664487 |
0.0000022 |
| 108.467056 |
1.653458 |
0.3746183 |
4.705612 |
0.0000025 |
0.0005702 |
ENSG00000227471.4 |
AKR1B15 |
FC_P |
AKR1B15 |
1.653458 |
0.0000025 |
| 689.124594 |
1.652816 |
0.2705632 |
6.098655 |
0.0000000 |
0.0000008 |
ENSG00000255150.1 |
EID3 |
FC_P |
EID3 |
1.652816 |
0.0000000 |
| 91.644442 |
1.647355 |
0.3299786 |
4.980873 |
0.0000006 |
0.0001848 |
ENSG00000233461.1 |
RP11-295G20.2 |
FC_P |
RP11.295G20.2 |
1.647355 |
0.0000006 |
| 640.385844 |
1.635229 |
0.2587414 |
6.309197 |
0.0000000 |
0.0000003 |
ENSG00000125775.10 |
SDCBP2 |
FC_P |
SDCBP2 |
1.635229 |
0.0000000 |
| 394.981996 |
1.633637 |
0.3342019 |
4.960803 |
0.0000007 |
0.0002002 |
ENSG00000137261.9 |
KIAA0319 |
FC_P |
KIAA0319 |
1.633637 |
0.0000007 |
| 324.554693 |
1.631043 |
0.3623638 |
4.530160 |
0.0000059 |
0.0011063 |
ENSG00000260604.1 |
RP1-140K8.5 |
FC_P |
RP1.140K8.5 |
1.631043 |
0.0000059 |
| 4.845477 |
1.623302 |
0.3768987 |
4.652562 |
0.0000033 |
0.0007079 |
ENSG00000253182.1 |
RP11-486M23.2 |
FC_P |
RP11.486M23.2 |
1.623302 |
0.0000033 |
| 305.596281 |
1.621391 |
0.3756554 |
4.353121 |
0.0000134 |
0.0019910 |
ENSG00000139144.5 |
PIK3C2G |
FC_P |
PIK3C2G |
1.621391 |
0.0000134 |
| 30.625669 |
1.619772 |
0.2995074 |
5.401982 |
0.0000001 |
0.0000276 |
ENSG00000207951.1 |
MIR561 |
FC_P |
MIR561 |
1.619772 |
0.0000001 |
| 15.391692 |
-1.611632 |
0.3769907 |
-4.671517 |
0.0000030 |
0.0006573 |
ENSG00000172782.7 |
FADS6 |
FC_P |
FADS6 |
-1.611632 |
0.0000030 |
| 28.058468 |
1.604897 |
0.3706982 |
4.327717 |
0.0000151 |
0.0021562 |
ENSG00000225365.1 |
AC078942.1 |
FC_P |
AC078942.1 |
1.604897 |
0.0000151 |
| 924.026965 |
1.594844 |
0.3112693 |
5.167927 |
0.0000002 |
0.0000823 |
ENSG00000152049.5 |
KCNE4 |
FC_P |
KCNE4 |
1.594844 |
0.0000002 |
| 130.255646 |
1.587408 |
0.3716887 |
4.140020 |
0.0000347 |
0.0039907 |
ENSG00000139352.3 |
ASCL1 |
FC_P |
ASCL1 |
1.587408 |
0.0000347 |
| 893.612664 |
1.584746 |
0.3066767 |
5.140070 |
0.0000003 |
0.0000928 |
ENSG00000141527.12 |
CARD14 |
FC_P |
CARD14 |
1.584746 |
0.0000003 |
| 56.094917 |
1.583818 |
0.3622893 |
4.529537 |
0.0000059 |
0.0011063 |
ENSG00000267097.1 |
RP11-309E23.2 |
FC_P |
RP11.309E23.2 |
1.583818 |
0.0000059 |
| 519.897668 |
1.579999 |
0.2686068 |
5.841001 |
0.0000000 |
0.0000030 |
ENSG00000140961.8 |
OSGIN1 |
FC_P |
OSGIN1 |
1.579999 |
0.0000000 |
| 434.077514 |
1.576655 |
0.3269303 |
4.774475 |
0.0000018 |
0.0004413 |
ENSG00000188660.3 |
LINC00319 |
FC_P |
LINC00319 |
1.576655 |
0.0000018 |
| 70.279417 |
1.574257 |
0.3572117 |
4.608540 |
0.0000041 |
0.0008361 |
ENSG00000237289.5 |
CKMT1B |
FC_P |
CKMT1B |
1.574257 |
0.0000041 |
| 40.675955 |
1.569777 |
0.3727069 |
4.209043 |
0.0000256 |
0.0032052 |
ENSG00000182256.8 |
GABRG3 |
FC_P |
GABRG3 |
1.569777 |
0.0000256 |
| 164.153848 |
-1.566624 |
0.3380011 |
-3.640008 |
0.0002726 |
0.0153539 |
ENSG00000178343.4 |
SHISA3 |
FC_P |
SHISA3 |
-1.566624 |
0.0002726 |
| 311.466074 |
1.561926 |
0.3236758 |
4.930127 |
0.0000008 |
0.0002238 |
ENSG00000168772.9 |
CXXC4 |
FC_P |
CXXC4 |
1.561926 |
0.0000008 |
| 4.667776 |
1.560918 |
0.3705970 |
4.465947 |
0.0000080 |
0.0013468 |
ENSG00000226122.1 |
AC018705.5 |
FC_P |
AC018705.5 |
1.560918 |
0.0000080 |
| 2.248005 |
1.558301 |
0.3652640 |
3.610291 |
0.0003059 |
0.0162947 |
ENSG00000249771.1 |
RP11-457P14.5 |
FC_P |
RP11.457P14.5 |
1.558301 |
0.0003059 |
| 53.491602 |
1.556404 |
0.3616656 |
4.663674 |
0.0000031 |
0.0006747 |
ENSG00000236345.1 |
RP11-59D5__B.2 |
FC_P |
RP11.59D5__B.2 |
1.556404 |
0.0000031 |
| 24.203147 |
1.545563 |
0.3759043 |
4.585414 |
0.0000045 |
0.0008986 |
ENSG00000253789.1 |
CTD-2571E19.1 |
FC_P |
CTD.2571E19.1 |
1.545563 |
0.0000045 |
| 18.804877 |
1.544589 |
0.3648193 |
3.977194 |
0.0000697 |
0.0063148 |
ENSG00000122711.4 |
SPINK4 |
FC_P |
SPINK4 |
1.544589 |
0.0000697 |
| 17.496912 |
1.543927 |
0.3641707 |
5.565284 |
0.0000000 |
0.0000118 |
ENSG00000236627.1 |
RP11-252P19.1 |
FC_P |
RP11.252P19.1 |
1.543927 |
0.0000000 |
| 3143.845023 |
1.541651 |
0.3770657 |
4.507479 |
0.0000066 |
0.0011794 |
ENSG00000108602.13 |
ALDH3A1 |
FC_P |
ALDH3A1 |
1.541651 |
0.0000066 |
| 12.035027 |
1.537615 |
0.3480180 |
4.377730 |
0.0000120 |
0.0018623 |
ENSG00000268791.1 |
AC093323.1 |
FC_P |
AC093323.1 |
1.537615 |
0.0000120 |
| 43.000719 |
1.535024 |
0.3611163 |
3.879784 |
0.0001045 |
0.0082697 |
ENSG00000117971.7 |
CHRNB4 |
FC_P |
CHRNB4 |
1.535024 |
0.0001045 |
| 718.846094 |
1.530922 |
0.2918438 |
5.188078 |
0.0000002 |
0.0000760 |
ENSG00000101311.11 |
FERMT1 |
FC_P |
FERMT1 |
1.530922 |
0.0000002 |
| 3439.676426 |
1.529067 |
0.2882660 |
5.296498 |
0.0000001 |
0.0000458 |
ENSG00000001084.6 |
GCLC |
FC_P |
GCLC |
1.529067 |
0.0000001 |
| 13.422176 |
1.527770 |
0.3526101 |
4.197867 |
0.0000269 |
0.0032823 |
ENSG00000234427.1 |
RP3-413H6.2 |
FC_P |
RP3.413H6.2 |
1.527770 |
0.0000269 |
| 388.632248 |
1.524274 |
0.3359375 |
4.568900 |
0.0000049 |
0.0009568 |
ENSG00000002726.15 |
AOC1 |
FC_P |
AOC1 |
1.524274 |
0.0000049 |
| 122.097272 |
1.523625 |
0.2904462 |
5.280863 |
0.0000001 |
0.0000494 |
ENSG00000271303.1 |
SRXN1 |
FC_P |
SRXN1 |
1.523625 |
0.0000001 |
| 162.336916 |
1.520657 |
0.3698228 |
4.272616 |
0.0000193 |
0.0026605 |
ENSG00000220154.2 |
RP11-46B11.2 |
FC_P |
RP11.46B11.2 |
1.520657 |
0.0000193 |
| 39.369008 |
1.519626 |
0.3308175 |
4.439335 |
0.0000090 |
0.0014901 |
ENSG00000230212.2 |
AP000688.14 |
FC_P |
AP000688.14 |
1.519626 |
0.0000090 |
| 24.272149 |
1.517845 |
0.3669766 |
4.669163 |
0.0000030 |
0.0006609 |
ENSG00000124102.4 |
PI3 |
FC_P |
PI3 |
1.517845 |
0.0000030 |
| 36.434622 |
1.513468 |
0.3750946 |
4.135713 |
0.0000354 |
0.0040229 |
ENSG00000260658.1 |
RP11-368L12.1 |
FC_P |
RP11.368L12.1 |
1.513468 |
0.0000354 |
| 7.562996 |
1.512713 |
0.3735174 |
3.947926 |
0.0000788 |
0.0067374 |
ENSG00000255993.1 |
PSMC1P9 |
FC_P |
PSMC1P9 |
1.512713 |
0.0000788 |
| 12.687357 |
1.511256 |
0.3673983 |
4.335138 |
0.0000146 |
0.0021095 |
ENSG00000146678.5 |
IGFBP1 |
FC_P |
IGFBP1 |
1.511256 |
0.0000146 |
| 71.579732 |
1.507560 |
0.3444255 |
4.263853 |
0.0000201 |
0.0027058 |
ENSG00000259425.1 |
RP11-566K19.5 |
FC_P |
RP11.566K19.5 |
1.507560 |
0.0000201 |
| 726.718346 |
1.506727 |
0.2870542 |
5.238100 |
0.0000002 |
0.0000598 |
ENSG00000166126.6 |
AMN |
FC_P |
AMN |
1.506727 |
0.0000002 |
| 3.503468 |
1.506585 |
0.3719346 |
4.048331 |
0.0000516 |
0.0052438 |
ENSG00000249887.1 |
RP11-457P14.6 |
FC_P |
RP11.457P14.6 |
1.506585 |
0.0000516 |
| 53.588664 |
-1.504691 |
0.3755506 |
-4.092375 |
0.0000427 |
0.0045854 |
ENSG00000189127.3 |
ANKRD34B |
FC_P |
ANKRD34B |
-1.504691 |
0.0000427 |
| 34.159138 |
-1.504641 |
0.3561157 |
-4.234575 |
0.0000229 |
0.0029739 |
ENSG00000206176.5 |
AC023490.1 |
FC_P |
AC023490.1 |
-1.504641 |
0.0000229 |
| 97.925630 |
1.504343 |
0.3757152 |
4.256290 |
0.0000208 |
0.0027785 |
ENSG00000201464.1 |
Y_RNA |
FC_P |
Y_RNA |
1.504343 |
0.0000208 |
| 4.532727 |
1.501453 |
0.3723273 |
4.033832 |
0.0000549 |
0.0054566 |
ENSG00000218813.1 |
RP11-59D5__B.3 |
FC_P |
RP11.59D5__B.3 |
1.501453 |
0.0000549 |
Pathway enrichment analysis fGSEA
Low SLC7A11 is the reference. When SLC7A11 is high, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)
## `summarise()` ungrouping output (override with `.groups` argument)
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='SLC7A11 low vs high')

kable(fgp)
| HALLMARK_MYC_TARGETS_V1 |
0.0013793 |
0.0048450 |
0.5760355 |
2.663927 |
0 |
189 |
up |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION |
0.0014225 |
0.0048450 |
0.5345159 |
2.429883 |
0 |
175 |
up |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY |
0.0015504 |
0.0048450 |
0.6106734 |
2.228717 |
0 |
46 |
up |
| HALLMARK_MYC_TARGETS_V2 |
0.0015385 |
0.0048450 |
0.5836289 |
2.207744 |
0 |
57 |
up |
| HALLMARK_MTORC1_SIGNALING |
0.0013812 |
0.0048450 |
0.4708370 |
2.175679 |
0 |
190 |
up |
| HALLMARK_E2F_TARGETS |
0.0013812 |
0.0048450 |
0.4544360 |
2.099844 |
0 |
191 |
up |
| HALLMARK_FATTY_ACID_METABOLISM |
0.0014286 |
0.0048450 |
0.4673342 |
2.075779 |
0 |
147 |
up |
| HALLMARK_GLYCOLYSIS |
0.0013774 |
0.0048450 |
0.4445459 |
2.055879 |
0 |
188 |
up |
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE |
0.0014599 |
0.0048450 |
0.4911549 |
2.052527 |
0 |
103 |
up |
| HALLMARK_XENOBIOTIC_METABOLISM |
0.0013774 |
0.0048450 |
0.4289172 |
1.983601 |
0 |
188 |
up |
| HALLMARK_G2M_CHECKPOINT |
0.0013870 |
0.0048450 |
0.4081273 |
1.881154 |
0 |
187 |
up |
| HALLMARK_P53_PATHWAY |
0.0013812 |
0.0048450 |
0.3842814 |
1.775717 |
0 |
190 |
up |
| HALLMARK_ESTROGEN_RESPONSE_LATE |
0.0013793 |
0.0048450 |
0.3800266 |
1.760757 |
0 |
193 |
up |
| HALLMARK_ESTROGEN_RESPONSE_EARLY |
0.0013812 |
0.0048450 |
0.3527743 |
1.630089 |
0 |
191 |
up |
| HALLMARK_ADIPOGENESIS |
0.0013870 |
0.0048450 |
0.3516720 |
1.618148 |
0 |
183 |
up |
| HALLMARK_DNA_REPAIR |
0.0014245 |
0.0048450 |
0.3592588 |
1.584524 |
0 |
141 |
up |
| HALLMARK_ALLOGRAFT_REJECTION |
0.0035587 |
0.0064935 |
-0.6380091 |
-3.203795 |
0 |
187 |
down |
| HALLMARK_INTERFERON_GAMMA_RESPONSE |
0.0036364 |
0.0064935 |
-0.6219276 |
-3.127702 |
0 |
194 |
down |
| HALLMARK_INTERFERON_ALPHA_RESPONSE |
0.0031056 |
0.0064935 |
-0.6655971 |
-3.038984 |
0 |
93 |
down |
| HALLMARK_IL6_JAK_STAT3_SIGNALING |
0.0029851 |
0.0064935 |
-0.5915983 |
-2.654658 |
0 |
82 |
down |
| HALLMARK_INFLAMMATORY_RESPONSE |
0.0036101 |
0.0064935 |
-0.5211774 |
-2.623153 |
0 |
193 |
down |
| HALLMARK_IL2_STAT5_SIGNALING |
0.0035971 |
0.0064935 |
-0.4470018 |
-2.246278 |
0 |
190 |
down |
| HALLMARK_COMPLEMENT |
0.0036101 |
0.0064935 |
-0.3962333 |
-1.994293 |
0 |
193 |
down |
| HALLMARK_KRAS_SIGNALING_UP |
0.0035971 |
0.0064935 |
-0.3913819 |
-1.966777 |
0 |
190 |
down |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB |
0.0036364 |
0.0064935 |
-0.3794807 |
-1.912989 |
0 |
195 |
down |
| HALLMARK_MYOGENESIS |
0.0035971 |
0.0064935 |
-0.3569952 |
-1.793976 |
0 |
190 |
down |
| HALLMARK_EPITHELIAL_MESENCHYMAL_TRANSITION |
0.0036101 |
0.0064935 |
-0.3546836 |
-1.773415 |
0 |
189 |
down |
| HALLMARK_PROTEIN_SECRETION |
0.0029586 |
0.0064935 |
0.3780810 |
1.544232 |
1 |
89 |
up |
| HALLMARK_APOPTOSIS |
0.0067114 |
0.0115714 |
-0.3245534 |
-1.594300 |
1 |
155 |
down |
| HALLMARK_PANCREAS_BETA_CELLS |
0.0272000 |
0.0453333 |
0.4285979 |
1.466396 |
16 |
36 |
up |
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='SLC7A11 low vs high')

kable(fgp)
| chr10q26 |
0.0014881 |
0.0183214 |
0.5331844 |
2.257309 |
0 |
108 |
up |
| chr1q41 |
0.0015798 |
0.0183214 |
0.5920613 |
2.213632 |
0 |
49 |
up |
| chr15q15 |
0.0014881 |
0.0183214 |
0.5171942 |
2.189613 |
0 |
108 |
up |
| chr4q25 |
0.0015974 |
0.0183214 |
0.5993173 |
2.174446 |
0 |
43 |
up |
| chr4q28 |
0.0017331 |
0.0183214 |
0.6667811 |
2.133799 |
0 |
25 |
up |
| chr15q26 |
0.0015291 |
0.0183214 |
0.4981181 |
2.079024 |
0 |
99 |
up |
| chr15q25 |
0.0015385 |
0.0183214 |
0.5104607 |
2.075108 |
0 |
84 |
up |
| chr6p24 |
0.0016367 |
0.0183214 |
0.5837631 |
2.062940 |
0 |
37 |
up |
| chr12q14 |
0.0016155 |
0.0183214 |
0.5366383 |
2.028993 |
0 |
56 |
up |
| chr2p25 |
0.0015649 |
0.0183214 |
0.5232161 |
2.021751 |
0 |
61 |
up |
| chr15q23 |
0.0016181 |
0.0183214 |
0.5576396 |
2.007328 |
0 |
42 |
up |
| chr13q32 |
0.0015773 |
0.0183214 |
0.5100048 |
1.997452 |
0 |
67 |
up |
| chr13q34 |
0.0016000 |
0.0183214 |
0.5283381 |
1.991566 |
0 |
54 |
up |
| chr20p12 |
0.0015873 |
0.0183214 |
0.5128631 |
1.963287 |
0 |
58 |
up |
| MT |
0.0016750 |
0.0183214 |
0.5741479 |
1.941781 |
0 |
31 |
up |
| chr15q22 |
0.0015723 |
0.0183214 |
0.4725615 |
1.906289 |
0 |
82 |
up |
| chr12q15 |
0.0016779 |
0.0183214 |
0.5526632 |
1.901309 |
0 |
34 |
up |
| chr17p11 |
0.0014684 |
0.0183214 |
0.4409642 |
1.879412 |
0 |
110 |
up |
| chr8p22 |
0.0017331 |
0.0183214 |
0.5862340 |
1.876037 |
0 |
25 |
up |
| chr4q12 |
0.0015823 |
0.0183214 |
0.4990676 |
1.872528 |
0 |
53 |
up |
| chr2q36 |
0.0015798 |
0.0183214 |
0.5056552 |
1.868338 |
0 |
46 |
up |
| chr2q37 |
0.0014286 |
0.0183214 |
0.4228101 |
1.866131 |
0 |
138 |
up |
| chr1q22 |
0.0015823 |
0.0183214 |
0.4956299 |
1.859630 |
0 |
53 |
up |
| chr12p11 |
0.0016207 |
0.0183214 |
0.5173659 |
1.852060 |
0 |
41 |
up |
| chr10q24 |
0.0014514 |
0.0183214 |
0.4184415 |
1.828484 |
0 |
127 |
up |
| chr15q24 |
0.0015456 |
0.0183214 |
0.4547009 |
1.812346 |
0 |
74 |
up |
| chr1q32 |
0.0013850 |
0.0183214 |
0.3973585 |
1.811982 |
0 |
174 |
up |
| chr2q21 |
0.0015773 |
0.0183214 |
0.4447608 |
1.713577 |
0 |
60 |
up |
| chr5q33 |
0.0028169 |
0.0208539 |
-0.5820298 |
-2.535771 |
0 |
77 |
down |
| chrYq11 |
0.0024691 |
0.0208539 |
-0.6315504 |
-2.276605 |
0 |
31 |
down |
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='SLC7A11 low vs high')

kable(fgp)
| FARMER_BREAST_CANCER_CLUSTER_1 |
0.0028818 |
0.0196461 |
-0.8260042 |
-3.247368 |
0 |
47 |
down |
| WINTER_HYPOXIA_DN |
0.0028011 |
0.0196461 |
-0.7893779 |
-3.098433 |
0 |
46 |
down |
| LEE_EARLY_T_LYMPHOCYTE_DN |
0.0028249 |
0.0196461 |
-0.7390486 |
-3.032090 |
0 |
57 |
down |
| REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES |
0.0028736 |
0.0196461 |
-0.7393387 |
-3.003432 |
0 |
55 |
down |
| WIELAND_UP_BY_HBV_INFECTION |
0.0031153 |
0.0196461 |
-0.6559711 |
-2.998066 |
0 |
95 |
down |
| FLECHNER_BIOPSY_KIDNEY_TRANSPLANT_REJECTED_VS_OK_UP |
0.0030960 |
0.0196461 |
-0.6732522 |
-2.962720 |
0 |
83 |
down |
| BASSO_CD40_SIGNALING_UP |
0.0031056 |
0.0196461 |
-0.6328562 |
-2.934267 |
0 |
100 |
down |
| MOSERLE_IFNA_RESPONSE |
0.0025773 |
0.0196461 |
-0.7977625 |
-2.910504 |
0 |
31 |
down |
| KEGG_HEMATOPOIETIC_CELL_LINEAGE |
0.0029499 |
0.0196461 |
-0.6521875 |
-2.862517 |
0 |
80 |
down |
| PID_CD8_TCR_PATHWAY |
0.0028818 |
0.0196461 |
-0.7084363 |
-2.841749 |
0 |
51 |
down |
| REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_BCR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS |
0.0029499 |
0.0196461 |
-0.6441142 |
-2.835918 |
0 |
81 |
down |
| BOSCO_INTERFERON_INDUCED_ANTIVIRAL_MODULE |
0.0029762 |
0.0196461 |
-0.6538299 |
-2.826034 |
0 |
74 |
down |
| HECKER_IFNB1_TARGETS |
0.0029851 |
0.0196461 |
-0.6220923 |
-2.825893 |
0 |
90 |
down |
| BROWNE_INTERFERON_RESPONSIVE_GENES |
0.0029412 |
0.0196461 |
-0.6713939 |
-2.818827 |
0 |
65 |
down |
| BIOCARTA_NKT_PATHWAY |
0.0025575 |
0.0196461 |
-0.8135376 |
-2.817425 |
0 |
26 |
down |
| KLEIN_TARGETS_OF_BCR_ABL1_FUSION |
0.0027397 |
0.0196461 |
-0.7571254 |
-2.817384 |
0 |
36 |
down |
| NAKAYAMA_SOFT_TISSUE_TUMORS_PCA1_UP |
0.0029240 |
0.0196461 |
-0.6426595 |
-2.812763 |
0 |
78 |
down |
| MORI_LARGE_PRE_BII_LYMPHOCYTE_DN |
0.0028571 |
0.0196461 |
-0.6848839 |
-2.793748 |
0 |
56 |
down |
| VILIMAS_NOTCH1_TARGETS_UP |
0.0028818 |
0.0196461 |
-0.7025690 |
-2.780732 |
0 |
49 |
down |
| BIOCARTA_CTLA4_PATHWAY |
0.0024814 |
0.0196461 |
-0.8352163 |
-2.779558 |
0 |
22 |
down |
| PID_TCR_PATHWAY |
0.0028653 |
0.0196461 |
-0.6683934 |
-2.776875 |
0 |
61 |
down |
| KEGG_PRIMARY_IMMUNODEFICIENCY |
0.0025773 |
0.0196461 |
-0.7611325 |
-2.776866 |
0 |
31 |
down |
| DUNNE_TARGETS_OF_AML1_MTG8_FUSION_UP |
0.0029070 |
0.0196461 |
-0.6924999 |
-2.748421 |
0 |
50 |
down |
| KEGG_LEISHMANIA_INFECTION |
0.0028653 |
0.0196461 |
-0.6426038 |
-2.743560 |
0 |
68 |
down |
| KUROZUMI_RESPONSE_TO_ONCOCYTIC_VIRUS |
0.0027855 |
0.0196461 |
-0.7059626 |
-2.728283 |
0 |
43 |
down |
| KEGG_INTESTINAL_IMMUNE_NETWORK_FOR_IGA_PRODUCTION |
0.0028818 |
0.0196461 |
-0.6931562 |
-2.725087 |
0 |
47 |
down |
| PID_IL12_2PATHWAY |
0.0028986 |
0.0196461 |
-0.6549167 |
-2.721004 |
0 |
63 |
down |
| PID_CD8_TCR_DOWNSTREAM_PATHWAY |
0.0028736 |
0.0196461 |
-0.6644365 |
-2.699155 |
0 |
55 |
down |
| REACTOME_INTERLEUKIN_2_FAMILY_SIGNALING |
0.0027100 |
0.0196461 |
-0.7138463 |
-2.690848 |
0 |
38 |
down |
| CROONQUIST_NRAS_SIGNALING_UP |
0.0026247 |
0.0196461 |
-0.7220709 |
-2.686291 |
0 |
35 |
down |
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='SLC7A11 low vs high')

kable(fgp)
| EPC1_TARGET_GENES |
0.0012270 |
0.0332968 |
0.4278147 |
2.071140 |
0 |
332 |
up |
| DLX6_TARGET_GENES |
0.0011848 |
0.0332968 |
0.4125402 |
2.058368 |
0 |
486 |
up |
| DLX4_TARGET_GENES |
0.0011403 |
0.0332968 |
0.3894230 |
1.997025 |
0 |
719 |
up |
| FOXO4_TARGET_GENES |
0.0012300 |
0.0332968 |
0.4118343 |
1.984089 |
0 |
314 |
up |
| DIDO1_TARGET_GENES |
0.0010593 |
0.0332968 |
0.3691100 |
1.956280 |
0 |
1381 |
up |
| ALKBH3_TARGET_GENES |
0.0012121 |
0.0332968 |
0.3996774 |
1.951342 |
0 |
382 |
up |
| GRHL1_TARGET_GENES |
0.0010627 |
0.0332968 |
0.3615587 |
1.915082 |
0 |
1334 |
up |
| ZNF711_TARGET_GENES |
0.0010604 |
0.0332968 |
0.3585655 |
1.902567 |
0 |
1465 |
up |
| CREB3L4_TARGET_GENES |
0.0010672 |
0.0332968 |
0.3603724 |
1.901884 |
0 |
1195 |
up |
| BARHL1_TARGET_GENES |
0.0010753 |
0.0332968 |
0.3605334 |
1.899527 |
0 |
1106 |
up |
| ZNF250_TARGET_GENES |
0.0011820 |
0.0332968 |
0.3777457 |
1.892073 |
0 |
512 |
up |
| FXR1_TARGET_GENES |
0.0010905 |
0.0332968 |
0.3604618 |
1.888812 |
0 |
1002 |
up |
| HNRNPH1_TARGET_GENES |
0.0010604 |
0.0332968 |
0.3540523 |
1.878376 |
0 |
1454 |
up |
| MXD1_TARGET_GENES |
0.0011682 |
0.0332968 |
0.3711710 |
1.869984 |
0 |
548 |
up |
| FOXG1_TARGET_GENES |
0.0011834 |
0.0332968 |
0.3733874 |
1.868001 |
0 |
508 |
up |
| SUPT20H_TARGET_GENES |
0.0010695 |
0.0332968 |
0.3514654 |
1.853684 |
0 |
1169 |
up |
| BANP_TARGET_GENES |
0.0011481 |
0.0332968 |
0.3618220 |
1.843724 |
0 |
635 |
up |
| KAT5_TARGET_GENES |
0.0011211 |
0.0332968 |
0.3567611 |
1.840118 |
0 |
768 |
up |
| ADA2_TARGET_GENES |
0.0011148 |
0.0332968 |
0.3541726 |
1.832291 |
0 |
801 |
up |
| KLF3_TARGET_GENES |
0.0011111 |
0.0332968 |
0.3542812 |
1.832139 |
0 |
794 |
up |
| NFE2L1_TARGET_GENES |
0.0012240 |
0.0332968 |
0.3747939 |
1.831210 |
0 |
394 |
up |
| HOXA1_TARGET_GENES |
0.0010917 |
0.0332968 |
0.3481950 |
1.824570 |
0 |
1005 |
up |
| SRPK1_TARGET_GENES |
0.0012361 |
0.0332968 |
0.3772523 |
1.817414 |
0 |
317 |
up |
| ATF5_TARGET_GENES |
0.0012121 |
0.0332968 |
0.3729002 |
1.815298 |
0 |
368 |
up |
| BARX1_TARGET_GENES |
0.0010823 |
0.0332968 |
0.3447329 |
1.813488 |
0 |
1074 |
up |
| ELF2_TARGET_GENES |
0.0011364 |
0.0332968 |
0.3526484 |
1.809987 |
0 |
722 |
up |
| ATF6_TARGET_GENES |
0.0010989 |
0.0332968 |
0.3462504 |
1.808447 |
0 |
918 |
up |
| HOXB6_TARGET_GENES |
0.0011710 |
0.0332968 |
0.3587852 |
1.803924 |
0 |
531 |
up |
| SETD1A_TARGET_GENES |
0.0010537 |
0.0332968 |
0.3401146 |
1.800749 |
0 |
1272 |
up |
| TEAD2_TARGET_GENES |
0.0010549 |
0.0332968 |
0.3393491 |
1.796229 |
0 |
1241 |
up |
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='SLC7A11 low vs high')

kable(fgp)
| GNF2_PA2G4 |
0.0014903 |
0.0098621 |
0.6163449 |
2.464975 |
0 |
75 |
up |
| GNF2_RAN |
0.0014793 |
0.0098621 |
0.6081434 |
2.463487 |
0 |
79 |
up |
| MORF_SOD1 |
0.0012563 |
0.0098621 |
0.5185047 |
2.450594 |
0 |
247 |
up |
| MORF_RFC4 |
0.0013624 |
0.0098621 |
0.5565803 |
2.444442 |
0 |
130 |
up |
| MORF_UNG |
0.0015083 |
0.0098621 |
0.6239810 |
2.441502 |
0 |
64 |
up |
| MORF_BUB3 |
0.0012579 |
0.0098621 |
0.5058740 |
2.388946 |
0 |
243 |
up |
| MORF_EI24 |
0.0013966 |
0.0098621 |
0.5532820 |
2.382313 |
0 |
119 |
up |
| MORF_PPP1CC |
0.0013228 |
0.0098621 |
0.5257248 |
2.358548 |
0 |
147 |
up |
| MORF_HAT1 |
0.0013210 |
0.0098621 |
0.5226613 |
2.356257 |
0 |
155 |
up |
| GNF2_RRM1 |
0.0014663 |
0.0098621 |
0.5653797 |
2.322414 |
0 |
86 |
up |
| MORF_DNMT1 |
0.0014245 |
0.0098621 |
0.5483406 |
2.319696 |
0 |
103 |
up |
| MORF_EIF3S2 |
0.0012658 |
0.0098621 |
0.4955697 |
2.317422 |
0 |
220 |
up |
| GNF2_SMC4L1 |
0.0014859 |
0.0098621 |
0.5706785 |
2.312354 |
0 |
80 |
up |
| GNF2_PCNA |
0.0015198 |
0.0098621 |
0.5910762 |
2.312306 |
0 |
65 |
up |
| MORF_HDAC2 |
0.0012563 |
0.0098621 |
0.4884997 |
2.308782 |
0 |
247 |
up |
| MORF_RRM1 |
0.0014684 |
0.0098621 |
0.5565185 |
2.295097 |
0 |
88 |
up |
| GNF2_MCM4 |
0.0015480 |
0.0098621 |
0.6053695 |
2.280582 |
0 |
52 |
up |
| MORF_CSNK2B |
0.0012516 |
0.0098621 |
0.4799630 |
2.276063 |
0 |
258 |
up |
| MODULE_286 |
0.0016260 |
0.0098621 |
0.6681389 |
2.271151 |
0 |
34 |
up |
| MORF_DAP3 |
0.0012937 |
0.0098621 |
0.4924239 |
2.269665 |
0 |
179 |
up |
| MORF_MTA1 |
0.0014556 |
0.0098621 |
0.5465058 |
2.268571 |
0 |
91 |
up |
| MORF_FEN1 |
0.0015576 |
0.0098621 |
0.5922271 |
2.255523 |
0 |
55 |
up |
| MODULE_235 |
0.0014706 |
0.0098621 |
0.5592473 |
2.250784 |
0 |
77 |
up |
| MORF_PRKDC |
0.0013441 |
0.0098621 |
0.4945365 |
2.243867 |
0 |
166 |
up |
| MORF_RAD23A |
0.0012315 |
0.0098621 |
0.4617755 |
2.226926 |
0 |
304 |
up |
| GNF2_CCNA2 |
0.0015198 |
0.0098621 |
0.5672663 |
2.219162 |
0 |
65 |
up |
| MODULE_54 |
0.0012658 |
0.0098621 |
0.4710572 |
2.218779 |
0 |
241 |
up |
| GNF2_NS |
0.0016340 |
0.0098621 |
0.6418281 |
2.218777 |
0 |
37 |
up |
| MORF_RAN |
0.0012626 |
0.0098621 |
0.4697997 |
2.216768 |
0 |
239 |
up |
| MORF_PTPN11 |
0.0014430 |
0.0098621 |
0.5290984 |
2.210565 |
0 |
94 |
up |
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='SLC7A11 low vs high')

kable(fgp)
| GO_T_CELL_RECEPTOR_COMPLEX |
0.0030211 |
0.0421001 |
-0.7926478 |
-3.617955 |
0 |
90 |
down |
| GO_POSITIVE_REGULATION_OF_LEUKOCYTE_CELL_CELL_ADHESION |
0.0037313 |
0.0421001 |
-0.5934269 |
-3.057276 |
0 |
209 |
down |
| GO_RESPONSE_TO_CHEMOKINE |
0.0030864 |
0.0421001 |
-0.6396210 |
-2.910984 |
0 |
89 |
down |
| GO_LYMPHOCYTE_MIGRATION |
0.0032258 |
0.0421001 |
-0.6272134 |
-2.870948 |
0 |
101 |
down |
| GO_POSITIVE_REGULATION_OF_LEUKOCYTE_DIFFERENTIATION |
0.0035336 |
0.0421001 |
-0.5857222 |
-2.846517 |
0 |
142 |
down |
| GO_POSITIVE_REGULATION_OF_LYMPHOCYTE_DIFFERENTIATION |
0.0030211 |
0.0421001 |
-0.6233623 |
-2.846017 |
0 |
91 |
down |
| GO_ALPHA_BETA_T_CELL_DIFFERENTIATION |
0.0031646 |
0.0421001 |
-0.6205015 |
-2.837391 |
0 |
98 |
down |
| GO_IMMUNE_RECEPTOR_ACTIVITY |
0.0034130 |
0.0421001 |
-0.5973635 |
-2.820265 |
0 |
120 |
down |
| GO_ALPHA_BETA_T_CELL_ACTIVATION |
0.0034843 |
0.0421001 |
-0.5829611 |
-2.806821 |
0 |
131 |
down |
| GO_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY |
0.0028736 |
0.0421001 |
-0.6629003 |
-2.785785 |
0 |
60 |
down |
| GO_B_CELL_RECEPTOR_SIGNALING_PATHWAY |
0.0032051 |
0.0421001 |
-0.6049015 |
-2.783731 |
0 |
103 |
down |
| GO_CYTOKINE_RECEPTOR_ACTIVITY |
0.0030211 |
0.0421001 |
-0.6082884 |
-2.777196 |
0 |
91 |
down |
| GO_T_CELL_SELECTION |
0.0027701 |
0.0421001 |
-0.7051419 |
-2.770701 |
0 |
46 |
down |
| GO_REGULATION_OF_LYMPHOCYTE_DIFFERENTIATION |
0.0038168 |
0.0421001 |
-0.5617022 |
-2.765002 |
0 |
162 |
down |
| GO_LYMPHOCYTE_CHEMOTAXIS |
0.0028902 |
0.0421001 |
-0.6667680 |
-2.743115 |
0 |
55 |
down |
| GO_REGULATION_OF_LEUKOCYTE_MEDIATED_CYTOTOXICITY |
0.0028986 |
0.0421001 |
-0.6273833 |
-2.735426 |
0 |
71 |
down |
| GO_REGULATION_OF_T_CELL_DIFFERENTIATION |
0.0034965 |
0.0421001 |
-0.5641702 |
-2.731206 |
0 |
134 |
down |
| GO_POSITIVE_REGULATION_OF_LEUKOCYTE_PROLIFERATION |
0.0034965 |
0.0421001 |
-0.5628371 |
-2.724752 |
0 |
134 |
down |
| GO_NEUTROPHIL_MIGRATION |
0.0032051 |
0.0421001 |
-0.5907828 |
-2.718757 |
0 |
103 |
down |
| GO_POSITIVE_REGULATION_OF_T_CELL_PROLIFERATION |
0.0030211 |
0.0421001 |
-0.5948595 |
-2.715885 |
0 |
91 |
down |
| GO_CD4_POSITIVE_ALPHA_BETA_T_CELL_DIFFERENTIATION |
0.0028986 |
0.0421001 |
-0.6191160 |
-2.713679 |
0 |
72 |
down |
| GO_ANTIGEN_BINDING |
0.0034965 |
0.0421001 |
-0.5581469 |
-2.702046 |
0 |
134 |
down |
| GO_CHEMOKINE_ACTIVITY |
0.0025840 |
0.0421001 |
-0.7025948 |
-2.700800 |
0 |
41 |
down |
| GO_B_CELL_PROLIFERATION |
0.0030030 |
0.0421001 |
-0.6078844 |
-2.694310 |
0 |
80 |
down |
| GO_REGULATION_OF_LEUKOCYTE_PROLIFERATION |
0.0038168 |
0.0421001 |
-0.5212359 |
-2.688158 |
0 |
213 |
down |
| GO_REGULATION_OF_CELL_KILLING |
0.0030488 |
0.0421001 |
-0.5873184 |
-2.673477 |
0 |
92 |
down |
| GO_POSITIVE_REGULATION_OF_CYTOKINE_BIOSYNTHETIC_PROCESS |
0.0028011 |
0.0421001 |
-0.6231760 |
-2.670943 |
0 |
64 |
down |
| GO_POSITIVE_REGULATION_OF_ANTIGEN_RECEPTOR_MEDIATED_SIGNALING_PATHWAY |
0.0023364 |
0.0421001 |
-0.8299386 |
-2.669134 |
0 |
20 |
down |
| GO_POSITIVE_REGULATION_OF_ALPHA_BETA_T_CELL_ACTIVATION |
0.0028653 |
0.0421001 |
-0.6344791 |
-2.660651 |
0 |
59 |
down |
| GO_T_CELL_MIGRATION |
0.0029240 |
0.0421001 |
-0.6442188 |
-2.658192 |
0 |
57 |
down |
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='SLC7A11 low vs high')

kable(fgp)
| RPS14_DN.V1_UP |
0.0040816 |
0.0192778 |
-0.5254744 |
-2.656141 |
0 |
182 |
down |
| NFE2L2.V2 |
0.0012516 |
0.0192778 |
0.5180769 |
2.548334 |
0 |
395 |
up |
| LEF1_UP.V1_UP |
0.0040816 |
0.0192778 |
-0.4209208 |
-2.111485 |
0 |
179 |
down |
| P53_DN.V2_UP |
0.0035714 |
0.0192778 |
-0.4315714 |
-2.102512 |
0 |
131 |
down |
| KRAS.LUNG_UP.V1_UP |
0.0033333 |
0.0192778 |
-0.4370391 |
-2.089853 |
0 |
119 |
down |
| HOXA9_DN.V1_UP |
0.0038023 |
0.0192778 |
-0.4154275 |
-2.073648 |
0 |
170 |
down |
| CYCLIN_D1_KE_.V1_DN |
0.0038610 |
0.0192778 |
-0.4037184 |
-2.013409 |
0 |
173 |
down |
| SNF5_DN.V1_UP |
0.0035971 |
0.0192778 |
-0.3899399 |
-1.939238 |
0 |
152 |
down |
| HINATA_NFKB_IMMU_INF |
0.0025253 |
0.0192778 |
-0.6698299 |
-1.918285 |
0 |
14 |
down |
| RPS14_DN.V1_DN |
0.0013495 |
0.0192778 |
0.4278120 |
1.913561 |
0 |
172 |
up |
| MYC_UP.V1_UP |
0.0013569 |
0.0192778 |
0.4187909 |
1.850271 |
0 |
157 |
up |
| KRAS.PROSTATE_UP.V1_UP |
0.0033445 |
0.0192778 |
-0.3847447 |
-1.843908 |
0 |
121 |
down |
| BRCA1_DN.V1_UP |
0.0033784 |
0.0192778 |
-0.3818200 |
-1.804937 |
0 |
111 |
down |
| RAF_UP.V1_DN |
0.0013175 |
0.0192778 |
0.3977018 |
1.797813 |
0 |
181 |
up |
| KRAS.KIDNEY_UP.V1_UP |
0.0035336 |
0.0192778 |
-0.3672899 |
-1.784366 |
0 |
130 |
down |
| KRAS.300_UP.V1_UP |
0.0035336 |
0.0192778 |
-0.3660896 |
-1.778534 |
0 |
130 |
down |
| ATM_DN.V1_DN |
0.0035842 |
0.0192778 |
-0.3635004 |
-1.766754 |
0 |
132 |
down |
| KRAS.600.LUNG.BREAST_UP.V1_UP |
0.0041841 |
0.0192778 |
-0.3335123 |
-1.746741 |
0 |
239 |
down |
| CAHOY_ASTROCYTIC |
0.0028409 |
0.0192778 |
0.4189906 |
1.740658 |
1 |
98 |
up |
| WNT_UP.V1_DN |
0.0036630 |
0.0192778 |
-0.3493423 |
-1.736856 |
0 |
155 |
down |
| KRAS.600_UP.V1_UP |
0.0042553 |
0.0192778 |
-0.3313137 |
-1.734246 |
0 |
244 |
down |
| ALK_DN.V1_DN |
0.0034130 |
0.0192778 |
-0.3587947 |
-1.731987 |
0 |
124 |
down |
| JNK_DN.V1_UP |
0.0038168 |
0.0192778 |
-0.3486267 |
-1.727245 |
0 |
161 |
down |
| STK33_SKM_UP |
0.0042017 |
0.0192778 |
-0.3285018 |
-1.724816 |
0 |
246 |
down |
| MEK_UP.V1_UP |
0.0013298 |
0.0192778 |
0.3813490 |
1.717274 |
0 |
175 |
up |
| PRC2_SUZ12_UP.V1_UP |
0.0039062 |
0.0192778 |
-0.3405697 |
-1.688198 |
0 |
166 |
down |
| KRAS.PROSTATE_UP.V1_DN |
0.0034247 |
0.0192778 |
-0.3411692 |
-1.663528 |
0 |
129 |
down |
| PTEN_DN.V1_DN |
0.0038610 |
0.0192778 |
-0.3341033 |
-1.652356 |
0 |
158 |
down |
| KRAS.300_UP.V1_DN |
0.0034014 |
0.0192778 |
-0.3350458 |
-1.628433 |
0 |
128 |
down |
| CSR_LATE_UP.V1_UP |
0.0013514 |
0.0192778 |
0.3657984 |
1.615817 |
0 |
156 |
up |
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='SLC7A11 low vs high')

kable(fgp)
| GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGG_BCELL_DN |
0.0035336 |
0.0114714 |
-0.7135214 |
-3.491817 |
0 |
159 |
down |
| GSE19888_ADENOSINE_A3R_INH_PRETREAT_AND_ACT_BY_A3R_VS_TCELL_MEMBRANES_ACT_MAST_CELL_UP |
0.0035587 |
0.0114714 |
-0.6463144 |
-3.248425 |
0 |
188 |
down |
| GSE10325_CD4_TCELL_VS_BCELL_UP |
0.0035842 |
0.0114714 |
-0.6197352 |
-3.132816 |
0 |
190 |
down |
| GSE7509_UNSTIM_VS_IFNA_STIM_IMMATURE_DC_DN |
0.0036232 |
0.0114714 |
-0.6293222 |
-3.111398 |
0 |
172 |
down |
| GSE7218_IGM_VS_IGG_SIGNAL_THGOUGH_ANTIGEN_BCELL_DN |
0.0036101 |
0.0114714 |
-0.6240050 |
-3.059563 |
0 |
163 |
down |
| GSE7509_UNSTIM_VS_FCGRIIB_STIM_DC_DN |
0.0036232 |
0.0114714 |
-0.6191177 |
-3.047398 |
0 |
168 |
down |
| GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_BCELL_UP |
0.0035587 |
0.0114714 |
-0.6054333 |
-3.042953 |
0 |
188 |
down |
| GSE24634_IL4_VS_CTRL_TREATED_NAIVE_CD4_TCELL_DAY3_DN |
0.0035842 |
0.0114714 |
-0.5908151 |
-2.963239 |
0 |
185 |
down |
| GSE43863_DAY6_EFF_VS_DAY150_MEM_LY6C_INT_CXCR5POS_CD4_TCELL_DN |
0.0035714 |
0.0114714 |
-0.5868038 |
-2.938842 |
0 |
182 |
down |
| GSE37533_PPARG1_FOXP3_VS_FOXP3_TRANSDUCED_CD4_TCELL_DN |
0.0035211 |
0.0114714 |
-0.5806766 |
-2.930705 |
0 |
189 |
down |
| GSE40685_TREG_VS_FOXP3_KO_TREG_PRECURSOR_DN |
0.0035842 |
0.0114714 |
-0.5744553 |
-2.903922 |
0 |
190 |
down |
| GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_6H_DN |
0.0036630 |
0.0114714 |
-0.5829122 |
-2.887333 |
0 |
176 |
down |
| GSE8835_CD4_VS_CD8_TCELL_CLL_PATIENT_UP |
0.0035842 |
0.0114714 |
-0.5743073 |
-2.882743 |
0 |
187 |
down |
| GSE1460_INTRATHYMIC_T_PROGENITOR_VS_CD4_THYMOCYTE_DN |
0.0035587 |
0.0114714 |
-0.5610281 |
-2.848183 |
0 |
194 |
down |
| GSE22886_NAIVE_CD8_TCELL_VS_MONOCYTE_UP |
0.0035842 |
0.0114714 |
-0.5619664 |
-2.840789 |
0 |
190 |
down |
| GSE29618_BCELL_VS_PDC_UP |
0.0035714 |
0.0114714 |
-0.5667642 |
-2.838479 |
0 |
182 |
down |
| GSE3039_NKT_CELL_VS_ALPHAALPHA_CD8_TCELL_DN |
0.0035842 |
0.0114714 |
-0.5599443 |
-2.830568 |
0 |
190 |
down |
| GSE25677_MPL_VS_R848_STIM_BCELL_DN |
0.0035971 |
0.0114714 |
-0.5699341 |
-2.822964 |
0 |
171 |
down |
| GSE19888_CTRL_VS_TCELL_MEMBRANES_ACT_MAST_CELL_PRETREAT_A3R_INH_DN |
0.0035971 |
0.0114714 |
-0.5552837 |
-2.809553 |
0 |
191 |
down |
| GSE18791_CTRL_VS_NEWCASTLE_VIRUS_DC_10H_DN |
0.0036364 |
0.0114714 |
-0.5657334 |
-2.804538 |
0 |
175 |
down |
| GSE19888_ADENOSINE_A3R_INH_VS_ACT_WITH_INHIBITOR_PRETREATMENT_IN_MAST_CELL_UP |
0.0035971 |
0.0114714 |
-0.5618989 |
-2.793575 |
0 |
178 |
down |
| GSE18791_UNSTIM_VS_NEWCATSLE_VIRUS_DC_10H_DN |
0.0036232 |
0.0114714 |
-0.5654195 |
-2.783087 |
0 |
168 |
down |
| GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_MYELOID_UP |
0.0036364 |
0.0114714 |
-0.5555162 |
-2.777806 |
0 |
183 |
down |
| GSE16450_CTRL_VS_IFNA_6H_STIM_IMMATURE_NEURON_CELL_LINE_DN |
0.0036364 |
0.0114714 |
-0.5598663 |
-2.775453 |
0 |
175 |
down |
| GSE26495_NAIVE_VS_PD1HIGH_CD8_TCELL_DN |
0.0035714 |
0.0114714 |
-0.5537996 |
-2.773550 |
0 |
182 |
down |
| GSE22886_NAIVE_CD8_TCELL_VS_DC_UP |
0.0035842 |
0.0114714 |
-0.5525306 |
-2.771223 |
0 |
185 |
down |
| GSE29618_BCELL_VS_PDC_DAY7_FLU_VACCINE_UP |
0.0036630 |
0.0114714 |
-0.5581082 |
-2.770479 |
0 |
180 |
down |
| GSE5589_LPS_AND_IL10_VS_LPS_AND_IL6_STIM_IL6_KO_MACROPHAGE_45MIN_UP |
0.0036364 |
0.0114714 |
-0.5530123 |
-2.765285 |
0 |
183 |
down |
| GSE7219_UNSTIM_VS_LPS_AND_ANTI_CD40_STIM_NIK_NFKB2_KO_DC_UP |
0.0036765 |
0.0114714 |
-0.5606645 |
-2.764469 |
0 |
173 |
down |
| GSE2706_UNSTIM_VS_2H_LPS_AND_R848_DC_DN |
0.0036630 |
0.0114714 |
-0.5553714 |
-2.756893 |
0 |
180 |
down |
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='SLC7A11 low vs high')

kable(fgp)
| GO_T_CELL_RECEPTOR_COMPLEX |
0.0030581 |
0.023721 |
-0.7926478 |
-3.567110 |
0 |
90 |
down |
| GSE7218_UNSTIM_VS_ANTIGEN_STIM_THROUGH_IGG_BCELL_DN |
0.0035211 |
0.023721 |
-0.7135214 |
-3.540442 |
0 |
159 |
down |
| LEE_DIFFERENTIATING_T_LYMPHOCYTE |
0.0035842 |
0.023721 |
-0.6954633 |
-3.490793 |
0 |
182 |
down |
| GNF2_ITGAL |
0.0027248 |
0.023721 |
-0.8209758 |
-3.338700 |
0 |
52 |
down |
| FARMER_BREAST_CANCER_CLUSTER_1 |
0.0025840 |
0.023721 |
-0.8260042 |
-3.291005 |
0 |
47 |
down |
| MODULE_292 |
0.0032468 |
0.023721 |
-0.6854026 |
-3.268075 |
0 |
124 |
down |
| GSE19888_ADENOSINE_A3R_INH_PRETREAT_AND_ACT_BY_A3R_VS_TCELL_MEMBRANES_ACT_MAST_CELL_UP |
0.0036232 |
0.023721 |
-0.6463144 |
-3.266836 |
0 |
188 |
down |
| REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL |
0.0034483 |
0.023721 |
-0.6435974 |
-3.240015 |
0 |
175 |
down |
| HALLMARK_ALLOGRAFT_REJECTION |
0.0036232 |
0.023721 |
-0.6380091 |
-3.220860 |
0 |
187 |
down |
| GNF2_PTPN4 |
0.0025381 |
0.023721 |
-0.8135020 |
-3.187351 |
0 |
44 |
down |
| MODULE_171 |
0.0032573 |
0.023721 |
-0.6540173 |
-3.170551 |
0 |
131 |
down |
| GSE7509_UNSTIM_VS_IFNA_STIM_IMMATURE_DC_DN |
0.0033784 |
0.023721 |
-0.6293222 |
-3.164707 |
0 |
172 |
down |
| GNF2_PTPRC |
0.0028571 |
0.023721 |
-0.7557365 |
-3.144730 |
0 |
59 |
down |
| GNF2_CD7 |
0.0024752 |
0.023721 |
-0.8385679 |
-3.125328 |
0 |
36 |
down |
| GSE10325_CD4_TCELL_VS_BCELL_UP |
0.0037313 |
0.023721 |
-0.6197352 |
-3.122983 |
0 |
190 |
down |
| GNF2_CASP1 |
0.0029412 |
0.023721 |
-0.6762542 |
-3.119118 |
0 |
103 |
down |
| MODULE_119 |
0.0033784 |
0.023721 |
-0.6374952 |
-3.117068 |
0 |
136 |
down |
| WINTER_HYPOXIA_DN |
0.0026247 |
0.023721 |
-0.7893779 |
-3.105401 |
0 |
46 |
down |
| GSE7509_UNSTIM_VS_FCGRIIB_STIM_DC_DN |
0.0034014 |
0.023721 |
-0.6191177 |
-3.097157 |
0 |
168 |
down |
| GSE7218_IGM_VS_IGG_SIGNAL_THGOUGH_ANTIGEN_BCELL_DN |
0.0035211 |
0.023721 |
-0.6240050 |
-3.095438 |
0 |
163 |
down |
| MODULE_436 |
0.0032258 |
0.023721 |
-0.6480472 |
-3.082104 |
0 |
123 |
down |
| GNF2_HCK |
0.0030303 |
0.023721 |
-0.6824185 |
-3.071791 |
0 |
89 |
down |
| GSE10325_LUPUS_CD4_TCELL_VS_LUPUS_BCELL_UP |
0.0036232 |
0.023721 |
-0.6054333 |
-3.060200 |
0 |
188 |
down |
| GNF2_ITGB2 |
0.0027248 |
0.023721 |
-0.7508068 |
-3.048282 |
0 |
51 |
down |
| MODULE_345 |
0.0030864 |
0.023721 |
-0.6454051 |
-3.047984 |
0 |
114 |
down |
| MODULE_208 |
0.0031546 |
0.023721 |
-0.6466721 |
-3.047519 |
0 |
117 |
down |
| LEE_EARLY_T_LYMPHOCYTE_DN |
0.0028571 |
0.023721 |
-0.7390486 |
-3.042654 |
0 |
57 |
down |
| REACTOME_CHEMOKINE_RECEPTORS_BIND_CHEMOKINES |
0.0028090 |
0.023721 |
-0.7393387 |
-3.035408 |
0 |
55 |
down |
| MODULE_361 |
0.0032258 |
0.023721 |
-0.6271367 |
-3.034143 |
0 |
130 |
down |
| HALLMARK_INTERFERON_ALPHA_RESPONSE |
0.0029762 |
0.023721 |
-0.6655971 |
-3.024076 |
0 |
93 |
down |